NM_016131.5:c.188+449A>G

Variant names:

• chr2-26099171-A-G
• rs9332419
• NM_016131.5:c.188+449A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016131.5(RAB10):​c.188+449A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,936 control chromosomes in the GnomAD database, including 17,668 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (17668 hom., cov: 32)
• Consequence: RAB10 NM_016131.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 9 publications found

Genes affected

RAB10 (HGNC:9759): (RAB10, member RAS oncogene family) RAB10 belongs to the RAS (see HRAS; MIM 190020) superfamily of small GTPases. RAB proteins localize to exocytic and endocytic compartments and regulate intracellular vesicle trafficking (Bao et al., 1998 [PubMed 9918381]).[supplied by OMIM, Mar 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB10	NM_016131.5	c.188+449A>G		intron_variant	Intron 2 of 5	ENST00000264710.5	NP_057215.3
RAB10	XM_047443004.1	c.173+449A>G		intron_variant	Intron 2 of 5		XP_047298960.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB10	ENST00000264710.5	c.188+449A>G		intron_variant	Intron 2 of 5	1	NM_016131.5	ENSP00000264710.4
RAB10	ENST00000462003.5	n.109+449A>G		intron_variant	Intron 2 of 5	4
RAB10	ENST00000473035.1	n.109+449A>G		intron_variant	Intron 2 of 5	4
RAB10	ENST00000495146.5	n.690+449A>G		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69455 AN: 151820 Hom.: 17666 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.0256

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.460

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.457 AC: 69473 AN: 151936 Hom.: 17668 Cov.: 32 AF XY: 0.450 AC XY: 33429 AN XY: 74242

African (AFR) AF: 0.290 AC: 12025 AN: 41406

American (AMR) AF: 0.366 AC: 5585 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3468

East Asian (EAS) AF: 0.0259 AC: 134 AN: 5174

South Asian (SAS) AF: 0.457 AC: 2201 AN: 4814

European-Finnish (FIN) AF: 0.571 AC: 6017 AN: 10536

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40168 AN: 67978

Other (OTH) AF: 0.460 AC: 968 AN: 2106

Alfa AF: 0.548 Hom.: 25711

Bravo AF: 0.432

Asia WGS AF: 0.264 AC: 916 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	8.6
DANN	Benign	0.75
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9332419; hg19: chr2-26322040;